Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.)

Ho-Huu et al. BMC Evolutionary Biology 2012, 12:195 http://www.biomedcentral.com/1471-2148/12/195 RESEARCH ARTICLE Open Access Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.) Joan Ho-Huu1, Joëlle Ronfort1, Stéphane De Mita1,2, Thomas Bataillon3, Isabelle Hochu1, Audrey Weber1 and Nathalie Chantret1* Abstract Background: Gene duplications are a molecular mechanism potentially mediating generation of functional novelty. However, the probabilities of maintenance and functional divergence of duplicated genes are shaped by selective pressures acting on gene copies immediately after the duplication event. The ratio of non-synonymous to synonymous substitution rates in protein-coding sequences provides a means to investigate selective pressures based on genic sequences. Three molecular signatures can reveal early stages of functional divergence between gene copies: change in the level of purifying selection between paralogous genes, occurrence of positive selection, and transient relaxed purifying selection following gene duplication. We studied three pairs of genes that are known to be involved in an interaction with symbiotic bacteria and were recently duplicated in the history of the Medicago genus (Fabaceae). We sequenced two pairs of polygalacturonase genes (Pg11-Pg3 and Pg11a-Pg11c) and one pair of auxine transporter-like genes (Lax2-Lax4) in 17 species belonging to the Medicago genus, and sought for molecular signatures of differentiation between copies. Results: Selective histories revealed by these three signatures of molecular differentiation were found to be markedly different between each pair of paralogs. We found sites under positive selection in the Pg11 paralogs while Pg3 has mainly evolved under purifying selection. The most recent paralogs examined Pg11a and Pg11c, are both undergoing positive selection and might be acquiring new functions. Lax2 and Lax4 paralogs are both under strong purifying selection, but still underwent a temporary relaxation of purifying selection immediately after duplication. Conclusions: This study illustrates the variety of selective pressures undergone by duplicated genes and the effect of age of the duplication. We found that relaxation of selective constraints immediately after duplication might promote adaptive divergence. Keywords: Duplication, Medicago, Neofunctionalization, Subfunctionalization, Paralogs evolution Background Gene duplications have long been hypothesized to be drivers of genome and gene function evolution [1]. Recently, availability of large-scale sequence data, and especially entire genome sequences, has brought significant support to this view [2,3]. In plants, duplications appear to be frequent and most lineages studied up to now have * Correspondence: 1 INRA - Institut National de la Recherche Agronomique, UMR AGAP, Montpellier 34060, France Full list of author information is available at the end of the article been affected by whole-genome duplication events (polyploidy) and/or segmental duplications [4-10]. Starting with Ohno, a range of models has been proposed to predict the fates of paralogous gene pairs resulting from duplications. These models can be categorized by their assumptions: they can be either neutral or involving natural selection, and can consider the early stage of duplication, i.e. when the duplication is not yet fixed in the species or start with the assumption that the gene duplication has just been fixed (recently reviewed in [11]). © 2012 Ho-Huu et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Ho-Huu et al. BMC Evolutionary Biology 2012, 12:195 http://www.biomedcentral.com/1471-2148/12/195 Immediately after the gene duplication event, the two copies are assumed to be identical and therefore functionally redundant. At this stage, there should be no selective pressure against any loss-of-function mutation affecting either copy. As a result, it is believed that most instances of gene duplications will eventually result in the loss of one of the copies (pseudogenization or nonfunctionalization). However, the relaxation of purifying selection (due to the initial redundancy) may allow some amount of divergence and occasionally can let one copy acquire a new function and be subsequently maintained by natural selection (neofunctionalization). This scenario is essential for the creative role of duplication envisioned by Ohno [1]. Force et al. [12] suggested that the presence of two redundant genes may drive the fixation of complementary degenerative mutations in both of copies, with higher probability in gene regulatory regions. At the end of this process, both gene copies are required to perform the set of functions originally performed by a single gene (subfunctionalization). These two scenarios are not mutually exclusive and may act jointly [13]. Besides these models, the maintenance of functionally redundant copies (without functional divergence) could be adaptive under specific circumstances, either through dosage effect or as a means of genetic robustness against deleterious mutations [14-16] and therefore also explain the fixation of duplications in species [11]. Functional analyses have been performed in order to determine the relative importance or the interaction between these different models. The occurrence and the characteristics of functional divergence of paralogous genes can be addressed either through the regulatory or protein-coding sequence angle. Whole-genome expression profiles revealed divergent expression patterns between paralogous gene pairs, providing indirect evidence for subfonctionalization and/or neofunctionalization [17]. Similar conclusions were also drawn from studies of polyploid species for which duplicated genes were instantly fixed in the species founder individual [18-20]. More specific and detailed functional analyses revealed several cases of paralogs undergoing neofunctionalization or subfunctionalization [21,22]. Beside differences in gene expression, rates of molecular evolution can be used to qualify the constraints experienced by genes. In particular, contrasting the rate of protein-changing (non-synonymous) substitution (dN) and the rate of silent (synonymous) substitution (dS) at the nucleotide level allows qualifying the type of selection acting on individual gene copies after a duplication event. The intensity of purifying selection is often estimated through the ratio ω = dN/dS. Values of ω < 1 are interpreted as evidence for purifying selection (the lower ω, the stronger purifying selection). Following pseudogenization, ω = 1 is expected (no constraint). Last, Page 2 of 13 amino acid sites exhibiting ω > 1 are li (...truncated)